Volatile organic compounds (VOCs) are significant metabolites that shape the aroma and flavor of fruit. This study investigated the VOC formation in three apple cultivars under two conditions: treatment with 1-methylcyclopropene (1-MCP) followed by storage at 0 °C, and storage at room temperature (RT) as a comparison. Gas chromatography-mass spectrometry (GC-MS) analysis of non-stored fruit identified esters, aldehydes, and alcohols as the predominant VOCs. Among cultivars, ‘Venus Golden’ and ‘Wanglin’ had significantly higher ester content than ‘Fuji’, while ‘Fuji’ exhibited higher aldehyde content. ‘Wanglin’ showed significantly higher alcohol content compared to the other two. Transcriptome analysis of ‘Fuji’ apples stored for 0, 2, and 4 weeks at RT identified 4990 differentially expressed genes (DEGs) during ripening. Comparison of samples stored at RT versus those treated with 1-MCP and stored at 0 ℃ for 2 and 4 weeks showed 7491 DEGs. Combining these datasets revealed 3532 unique DEGs. KEGG pathway analysis indicated enrichment in pathways related to energy, carbohydrate, lipid, amino acid, and terpenoid metabolism. O2PLS analysis identified 10 DEGs potentially involved in VOC formation in ‘Fuji’. Analysis of VOC-related gene expression in ‘Venus Golden’ and ‘Wanglin’ showed cultivar-specific responses, particularly in genes encoding phenylalanine ammonia lyase (PAL) and lipoxygenase (LOX). These findings suggest that the effects of 1-MCP treatment combined with 0 ℃ storage on VOC formation vary among apple cultivars and are associated with differential expression of PAL and LOX genes. This study provides insights into the molecular mechanisms governing post-harvest regulation of apple fruit aroma and flavor.